Onconova Implementation Guide - Local Development build (v0.2.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

• Content
• Detailed Descriptions
• Mappings
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Resource Profile: Genomic Variant Profile

A profile representing a genomic variant identified for a cancer patient.

This profile extends the base mCODE GenomicVariant profile (which in turn profiles the Genomics Reporting Variant profile) to include specific constraints and extensions relevant to Onconova.

Conformance:

Observation resources representing a genomic variant in the scope of Onconova SHALL conform to this profile. Any resource intended to conform to this profile SHOULD populate meta.profile accordingly.

Usages:

• Refer to this Profile: Molecular Tumor Board Therapeutic Recommendation
• CapabilityStatements using this Profile: Onconova FHIR REST Server Capability Statement

You can also check for usages in the FHIR IG Statistics

Formal Views of Profile Content

Description of Profiles, Differentials, Snapshots and how the different presentations work.

• Key Elements Table
• Differential Table
• Snapshot Table
• Statistics/References
• All

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicVariant	Variant Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension				Content/Rules for all slices
extension:secondary-finding		0..1	CodeableConcept	Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:genomic-variant-assessment-date	SO	0..1	dateTime	Genomic Variant Assessment Date URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!SΣ	1..1	code	Not used in this profile Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category	S	1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
coding	Σ	1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
code	SΣ	1..1	CodeableConcept	69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69548-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
subject	SOΣ	1..1	Reference(Cancer Patient Profile)	Who and/or what the observation is about Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
focus	Σ	0..*	Reference(Resource)	Not used in this profile
encounter	Σ	0..1	Reference(Encounter)	Not used in this profile
Slices for effective[x]	SΣ	1..1	dateTime	Clinically-relevant date of the genomic variant (e.g. the specimen collection date) Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SOΣ	0..1	dateTime	Clinically relevant time/time-period for observation Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
issued	Σ	0..1	instant	Not used in this profile
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Not used in this profile
Slices for value[x]	SΣC	0..1	CodeableConcept	Actual result Slice: Unordered, Closed by type:$this
value[x]:valueCodeableConcept	ΣC	0..1	CodeableConcept	Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required)
dataAbsentReason	SC	0..1	CodeableConcept	Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	Not used in this profile Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
bodySite		0..1	CodeableConcept	Not used in this profile Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method	S	0..1	CodeableConcept	Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible)
specimen	S	0..1	Reference(Human Specimen Profile)	Not used in this profile
device		0..1	Reference(Device | DeviceMetric)	Not used in this profile
Slices for component	SΣ	4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string	Σ	0..1	BackboneElement	Not used in this profile
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:gene-studied	SΣ	0..*	BackboneElement	Gene Studied
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
component:cytogenetic-location	SOΣ	0..*	BackboneElement	Cytogenetic (Chromosome) Location Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Example: 1q21.1
component:reference-sequence-assembly	OΣ	0..*	BackboneElement	Human Reference Sequence Assembly Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
component:coding-hgvs	OΣ	0..1	BackboneElement	Coding (cDNA) Change - cHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48004-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
component:genomic-hgvs	SOΣ	0..1	BackboneElement	Genomic (gDNA) Change - gHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81290-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
component:cytogenomic-nomenclature	SΣ	0..1	BackboneElement	Cytogenomic Nomenclature (ISCN)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81291-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Actual component result Binding Description: (example): Binding not yet defined
component:genomic-ref-seq	OΣ	0..1	BackboneElement	Genomic Reference Sequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48013-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned genomic reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
component:transcript-ref-seq	OΣ	0..1	BackboneElement	Reference Transcript Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 51958-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned transcript reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
component:exact-start-end	OΣ	0..1	BackboneElement	Exact Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81254-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:inner-start-end	OΣ	0..1	BackboneElement	Inner Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81302-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:outer-start-end	OΣ	0..1	BackboneElement	Outer Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81301-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:coordinate-system	OΣ	0..1	BackboneElement	Coordinate System Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 92822-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible)
component:ref-allele	Σ	0..1	BackboneElement	Not used in this profile
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69547-8
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:alt-allele	Σ	0..1	BackboneElement	Not used in this profile
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69551-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:coding-change-type	SOΣ	0..1	BackboneElement	Coding DNA Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48019-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: Coding DNA Change Types Value Set (required)
component:genomic-source-class	SOΣ	0..1	BackboneElement	Genomic Source Class Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48002-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible)
component:sample-allelic-frequency	SOΣ	0..1	BackboneElement	Sample Allelic Frequency Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81258-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	Quantity	Relative frequency in the sample
comparator	?!Σ	0..1	code	< | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented.
system	ΣC	0..1	uri	System that defines coded unit form Required Pattern: http://unitsofmeasure.org
component:allelic-read-depth	OΣ	0..1	BackboneElement	Allelic Read Depth Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82121-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:allelic-state	SOΣ	0..1	BackboneElement	Allelic State Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 53034-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible)
component:variant-inheritance	OΣ	0..1	BackboneElement	Variant Inheritance Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-inheritance
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Maternal | Paternal | Unknown Binding: Variant Inheritances (extensible)
component:variation-code	SOΣ	0..*	BackboneElement	Variation Code Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81252-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	ClinVar ID or similar Binding Description: (example): Multiple bindings acceptable
component:chromosome-identifier	OΣ	0..*	BackboneElement	Chromosome Identifier Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48000-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
component:protein-hgvs	SOΣ	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48005-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
component:amino-acid-change-type	SOΣ	0..1	BackboneElement	Amino Acid Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48006-1 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48006-1
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent Binding: Amino Acid Change Type Value Set (required)
component:molecular-consequence	SOΣ	0..1	BackboneElement	Molecular Consequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	molecular-consequence Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: molecular-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
component:copy-number	SOΣ	0..1	BackboneElement	Genomic Structural Variant Copy Number Obligations Actor SHALL:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82155-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣC	0..1	Quantity	Actual component result Constraints: cnt-3
component:variant-confidence-status	OΣ	0..1	BackboneElement	Variant Confidence Status Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-confidence-status
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	High | Intermediate | Low Binding: Variant Confidence Status (required)
component:clinical-relevance	SOΣ	1..1	BackboneElement	Clinical relevance of the genomic variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LL4034-6
display		1..1	string	Representation defined by the system Fixed Value: ACMG_Clinical significance of genetic variation
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	Actual component result Binding: Clinical Relevance Value Set (required)
component:nucleotides-count	SOΣ	1..1	BackboneElement	Length of of the variant in nNucleotides Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C709
display		1..1	string	Representation defined by the system Fixed Value: Nucleotides
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	integer	Actual component result
component:gene-region	SOΣ	1..1	BackboneElement	Region (exon, intron, etc.) of the gene affected by the variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova) MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C13445
display		1..1	string	Representation defined by the system Fixed Value: Gene Feature
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
component:gene-panel-sequencing	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C165600
display		1..1	string	Representation defined by the system Fixed Value: Tumor Panel Sequencing
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Sequencing Gene Panel
component:hgvs-version	SOΣ	1..1	BackboneElement	HGVS Version Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81303-0
display		1..1	string	Representation defined by the system Fixed Value: HGVS version [ID]
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
component:rna-hgvs	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: rna-hgvs
display		1..1	string	Representation defined by the system Fixed Value: Transcript RNA change (rHGVS)
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.status	Base	required	ObservationStatus	📍4.0.1	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.value[x]:valueCodeableConcept	Base	required	LOINC Answer Codes for LL1971-2	∅	unknown?
Observation.dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📦4.0.1	FHIR Std.
Observation.method	Base	extensible	LOINC Answer Codes for LL4048-6	∅	unknown?
Observation.component.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	LOINC Answer Codes for LL1040-6	∅	unknown?
Observation.component:coding-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenomic-nomenclature.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x]	Base	example		Not State	Unknown
Observation.component:genomic-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:transcript-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:exact-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​value[x]	Base	extensible	LOINC Answer Codes for LL5323-2	∅	unknown?
Observation.component:ref-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​value[x]	Base	required	Coding DNA Change Types Value Set	📦0.2.0	This IG
Observation.component:genomic-source-class.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​value[x]	Base	extensible	LOINC Answer Codes for LL378-1	∅	unknown?
Observation.component:sample-allelic-frequency.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator	Base	required	QuantityComparator	📍4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​value[x]	Base	extensible	LOINC Answer Codes for LL381-5	∅	unknown?
Observation.component:variant-inheritance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​value[x]	Base	extensible	Variant Inheritances	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:variation-code.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variation-code.​value[x]	Base	example		Not State	Unknown
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	LOINC Answer Codes for LL2938-0	∅	unknown?
Observation.component:protein-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:amino-acid-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​value[x]	Base	required	Amino Acid Change Type Value Set	📦0.2.0	This IG
Observation.component:molecular-consequence.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​value[x]	Base	extensible	Molecular Consequence	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:copy-number.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​value[x]	Base	required	Variant Confidence Status	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:clinical-relevance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​value[x]	Base	required	Clinical Relevance Value Set	📦0.2.0	This IG
Observation.component:nucleotides-count.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-region.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.

Constraints

Id	Grade	Path(s)	Description	Expression
cnt-3	error	Observation.component:copy-number.value[x]	There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.	(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both	extension.exists() != value.exists()
o-var-req-1	error	Observation	The subject element is required and must be provided.	subject.exists() and subject.resolve().is(Patient)
o-var-req-2	error	Observation	The effectiveDateTime element is required and must be provided.	effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3	error	Observation	The genes extension is required and must be provided.	component.where(code.coding.code = '48018-6').exists()
o-var-req-4	error	Observation	At least one HGVS representation (coding, protein, or genomic) must be provided.	component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicVariant	Variant Constraints: o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
Slices for extension				Content/Rules for all slices
extension:genomic-variant-assessment-date	SO	0..1	dateTime	Genomic Variant Assessment Date URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
status		1..1	code	Not used in this profile
subject	O	1..1	Reference(Cancer Patient Profile)	Who and/or what the observation is about Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
focus		0..*	Reference(Resource)	Not used in this profile
encounter		0..1	Reference(Encounter)	Not used in this profile
effective[x]		1..1	dateTime	Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
Slices for effective[x]				Content/Rules for all slices
effective[x]:effectiveDateTime	O	0..1	dateTime	Clinically relevant time/time-period for observation Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
issued		0..1	instant	Not used in this profile
performer		0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Not used in this profile
interpretation		0..*	CodeableConcept	Not used in this profile
bodySite		0..1	CodeableConcept	Not used in this profile
specimen		0..1	Reference(Human Specimen Profile)	Not used in this profile
device		0..1	Reference(Device | DeviceMetric)	Not used in this profile
component		4..*	BackboneElement	Component results
Slices for component				Content/Rules for all slices
component:conclusion-string		0..1	BackboneElement	Not used in this profile
component:cytogenetic-location	O	0..*	BackboneElement	Cytogenetic (Chromosome) Location Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:reference-sequence-assembly	O	0..*	BackboneElement	Human Reference Sequence Assembly Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:coding-hgvs	O	0..1	BackboneElement	Coding (cDNA) Change - cHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
component:genomic-hgvs	O	0..1	BackboneElement	Genomic (gDNA) Change - gHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
component:genomic-ref-seq	O	0..1	BackboneElement	Genomic Reference Sequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:transcript-ref-seq	O	0..1	BackboneElement	Reference Transcript Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:exact-start-end	O	0..1	BackboneElement	Exact Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:inner-start-end	O	0..1	BackboneElement	Inner Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:outer-start-end	O	0..1	BackboneElement	Outer Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:coordinate-system	O	0..1	BackboneElement	Coordinate System Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:ref-allele		0..1	BackboneElement	Not used in this profile
component:alt-allele		0..1	BackboneElement	Not used in this profile
component:coding-change-type	O	0..1	BackboneElement	Coding DNA Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: Coding DNA Change Types Value Set (required)
component:genomic-source-class	O	0..1	BackboneElement	Genomic Source Class Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:sample-allelic-frequency	O	0..1	BackboneElement	Sample Allelic Frequency Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:allelic-read-depth	O	0..1	BackboneElement	Allelic Read Depth Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:allelic-state	O	0..1	BackboneElement	Allelic State Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:variant-inheritance	O	0..1	BackboneElement	Variant Inheritance Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:variation-code	O	0..*	BackboneElement	Variation Code Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:chromosome-identifier	O	0..*	BackboneElement	Chromosome Identifier Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:protein-hgvs	O	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
component:amino-acid-change-type	O	0..1	BackboneElement	Amino Acid Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent Binding: Amino Acid Change Type Value Set (required)
component:molecular-consequence	O	0..1	BackboneElement	Molecular Consequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:copy-number	O	0..1	BackboneElement	Genomic Structural Variant Copy Number Obligations Actor SHALL:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:variant-confidence-status	O	0..1	BackboneElement	Variant Confidence Status Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:clinical-relevance	SO	1..1	BackboneElement	Clinical relevance of the genomic variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LL4034-6
display		1..1	string	Representation defined by the system Fixed Value: ACMG_Clinical significance of genetic variation
value[x]	S	0..1	CodeableConcept	Actual component result Binding: Clinical Relevance Value Set (required)
component:nucleotides-count	SO	1..1	BackboneElement	Length of of the variant in nNucleotides Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C709
display		1..1	string	Representation defined by the system Fixed Value: Nucleotides
value[x]	S	0..1	integer	Actual component result
component:gene-region	SO	1..1	BackboneElement	Region (exon, intron, etc.) of the gene affected by the variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova) MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C13445
display		1..1	string	Representation defined by the system Fixed Value: Gene Feature
value[x]	S	0..1	string	Actual component result
component:gene-panel-sequencing	SO	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C165600
display		1..1	string	Representation defined by the system Fixed Value: Tumor Panel Sequencing
value[x]	S	0..1	string	Sequencing Gene Panel
component:hgvs-version	SO	1..1	BackboneElement	HGVS Version Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81303-0
display		1..1	string	Representation defined by the system Fixed Value: HGVS version [ID]
value[x]	S	0..1	string	Actual component result
component:rna-hgvs	SO	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
code		1..1	code	Symbol in syntax defined by the system Fixed Value: rna-hgvs
display		1..1	string	Representation defined by the system Fixed Value: Transcript RNA change (rHGVS)
value[x]	S	0..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Observation.component:coding-change-type.​value[x]	Base	required	Coding DNA Change Types Value Set	📦0.2.0	This IG
Observation.component:amino-acid-change-type.​value[x]	Base	required	Amino Acid Change Type Value Set	📦0.2.0	This IG
Observation.component:clinical-relevance.​value[x]	Base	required	Clinical Relevance Value Set	📦0.2.0	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
o-var-req-1	error	Observation	The subject element is required and must be provided.	subject.exists() and subject.resolve().is(Patient)
o-var-req-2	error	Observation	The effectiveDateTime element is required and must be provided.	effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3	error	Observation	The genes extension is required and must be provided.	component.where(code.coding.code = '48018-6').exists()
o-var-req-4	error	Observation	At least one HGVS representation (coding, protein, or genomic) must be provided.	component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicVariant	Variant Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:secondary-finding		0..1	CodeableConcept	Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:genomic-variant-assessment-date	SO	0..1	dateTime	Genomic Variant Assessment Date URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Business Identifier for observation
basedOn	Σ	0..*	Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)	Fulfills plan, proposal or order
partOf	Σ	0..*	Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)	Part of referenced event
status	?!SΣ	1..1	code	Not used in this profile Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category	S	1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding	Σ	1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
code	SΣ	1..1	CodeableConcept	69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69548-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
subject	SOΣ	1..1	Reference(Cancer Patient Profile)	Who and/or what the observation is about Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
focus	Σ	0..*	Reference(Resource)	Not used in this profile
encounter	Σ	0..1	Reference(Encounter)	Not used in this profile
Slices for effective[x]	SΣ	1..1	dateTime	Clinically-relevant date of the genomic variant (e.g. the specimen collection date) Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SOΣ	0..1	dateTime	Clinically relevant time/time-period for observation Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
issued	Σ	0..1	instant	Not used in this profile
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Not used in this profile
Slices for value[x]	SΣC	0..1	CodeableConcept	Actual result Slice: Unordered, Closed by type:$this
value[x]:valueCodeableConcept	ΣC	0..1	CodeableConcept	Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required)
dataAbsentReason	SC	0..1	CodeableConcept	Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	Not used in this profile Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
note		0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
bodySite		0..1	CodeableConcept	Not used in this profile Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method	S	0..1	CodeableConcept	Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible)
specimen	S	0..1	Reference(Human Specimen Profile)	Not used in this profile
device		0..1	Reference(Device | DeviceMetric)	Not used in this profile
referenceRange	C	0..*	BackboneElement	Not used in this profile Constraints: obs-3
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
low	C	0..1	SimpleQuantity	Low Range, if relevant
high	C	0..1	SimpleQuantity	High Range, if relevant
type		0..1	CodeableConcept	Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo		0..*	CodeableConcept	Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age		0..1	Range	Applicable age range, if relevant
text		0..1	string	Text based reference range in an observation
hasMember	Σ	0..*	Reference(Observation | QuestionnaireResponse | MolecularSequence)	Not used in this profile
derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from
Slices for component	SΣ	4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x]	Σ	0..1		Actual component result
valueQuantity			Quantity
valueCodeableConcept			CodeableConcept
valueString			string
valueBoolean			boolean
valueInteger			integer
valueRange			Range
valueRatio			Ratio
valueSampledData			SampledData
valueTime			time
valueDateTime			dateTime
valuePeriod			Period
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:conclusion-string	Σ	0..1	BackboneElement	Not used in this profile
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Summary conclusion (interpretation/impression)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-studied	SΣ	0..*	BackboneElement	Gene Studied
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:cytogenetic-location	SOΣ	0..*	BackboneElement	Cytogenetic (Chromosome) Location Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Example: 1q21.1
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:reference-sequence-assembly	OΣ	0..*	BackboneElement	Human Reference Sequence Assembly Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:coding-hgvs	OΣ	0..1	BackboneElement	Coding (cDNA) Change - cHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48004-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:genomic-hgvs	SOΣ	0..1	BackboneElement	Genomic (gDNA) Change - gHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81290-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:cytogenomic-nomenclature	SΣ	0..1	BackboneElement	Cytogenomic Nomenclature (ISCN)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81291-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Actual component result Binding Description: (example): Binding not yet defined
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:genomic-ref-seq	OΣ	0..1	BackboneElement	Genomic Reference Sequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48013-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned genomic reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:transcript-ref-seq	OΣ	0..1	BackboneElement	Reference Transcript Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 51958-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned transcript reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:exact-start-end	OΣ	0..1	BackboneElement	Exact Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81254-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Range	Range in question. 'High' can be omitted for single nucleotide variants.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:inner-start-end	OΣ	0..1	BackboneElement	Inner Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81302-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Range	Imprecise variant inner-bounding range
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:outer-start-end	OΣ	0..1	BackboneElement	Outer Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81301-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Range	Imprecise variant outer-bounding range
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:coordinate-system	OΣ	0..1	BackboneElement	Coordinate System Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 92822-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:ref-allele	Σ	0..1	BackboneElement	Not used in this profile
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69547-8
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Normalized string per the VCF format.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:alt-allele	Σ	0..1	BackboneElement	Not used in this profile
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69551-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Normalized string per the VCF format.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:coding-change-type	SOΣ	0..1	BackboneElement	Coding DNA Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48019-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: Coding DNA Change Types Value Set (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:genomic-source-class	SOΣ	0..1	BackboneElement	Genomic Source Class Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48002-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:sample-allelic-frequency	SOΣ	0..1	BackboneElement	Sample Allelic Frequency Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81258-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	Quantity	Relative frequency in the sample
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
value	Σ	0..1	decimal	Numerical value (with implicit precision)
comparator	?!Σ	0..1	code	< | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented.
unit	Σ	0..1	string	Unit representation
system	ΣC	0..1	uri	System that defines coded unit form Required Pattern: http://unitsofmeasure.org
code	Σ	0..1	code	Coded form of the unit
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:allelic-read-depth	OΣ	0..1	BackboneElement	Allelic Read Depth Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82121-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Quantity	Unfiltered count of supporting reads
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:allelic-state	SOΣ	0..1	BackboneElement	Allelic State Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 53034-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:variant-inheritance	OΣ	0..1	BackboneElement	Variant Inheritance Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-inheritance
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Maternal | Paternal | Unknown Binding: Variant Inheritances (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:variation-code	SOΣ	0..*	BackboneElement	Variation Code Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81252-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	ClinVar ID or similar Binding Description: (example): Multiple bindings acceptable
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:chromosome-identifier	OΣ	0..*	BackboneElement	Chromosome Identifier Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48000-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:protein-hgvs	SOΣ	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48005-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:amino-acid-change-type	SOΣ	0..1	BackboneElement	Amino Acid Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48006-1 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48006-1
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent Binding: Amino Acid Change Type Value Set (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:molecular-consequence	SOΣ	0..1	BackboneElement	Molecular Consequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	molecular-consequence Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: molecular-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:copy-number	SOΣ	0..1	BackboneElement	Genomic Structural Variant Copy Number Obligations Actor SHALL:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82155-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣC	0..1	Quantity	Actual component result Constraints: cnt-3
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:variant-confidence-status	OΣ	0..1	BackboneElement	Variant Confidence Status Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-confidence-status
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	High | Intermediate | Low Binding: Variant Confidence Status (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:clinical-relevance	SOΣ	1..1	BackboneElement	Clinical relevance of the genomic variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LL4034-6
display		1..1	string	Representation defined by the system Fixed Value: ACMG_Clinical significance of genetic variation
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	Actual component result Binding: Clinical Relevance Value Set (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:nucleotides-count	SOΣ	1..1	BackboneElement	Length of of the variant in nNucleotides Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C709
display		1..1	string	Representation defined by the system Fixed Value: Nucleotides
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	integer	Actual component result
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-region	SOΣ	1..1	BackboneElement	Region (exon, intron, etc.) of the gene affected by the variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova) MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C13445
display		1..1	string	Representation defined by the system Fixed Value: Gene Feature
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-panel-sequencing	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C165600
display		1..1	string	Representation defined by the system Fixed Value: Tumor Panel Sequencing
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Sequencing Gene Panel
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:hgvs-version	SOΣ	1..1	BackboneElement	HGVS Version Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81303-0
display		1..1	string	Representation defined by the system Fixed Value: HGVS version [ID]
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:rna-hgvs	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: rna-hgvs
display		1..1	string	Representation defined by the system Fixed Value: Transcript RNA change (rHGVS)
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.language	Base	preferred	Common Languages	📦4.0.1	FHIR Std.
Observation.status	Base	required	ObservationStatus	📍4.0.1	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.value[x]:valueCodeableConcept	Base	required	LOINC Answer Codes for LL1971-2	∅	unknown?
Observation.dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📦4.0.1	FHIR Std.
Observation.method	Base	extensible	LOINC Answer Codes for LL4048-6	∅	unknown?
Observation.referenceRange.​type	Base	preferred	Observation Reference Range Meaning Codes	📦4.0.1	FHIR Std.
Observation.referenceRange.​appliesTo	Base	example	Observation Reference Range Applies To Codes	📦4.0.1	FHIR Std.
Observation.component.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:gene-studied.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:cytogenetic-location.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	LOINC Answer Codes for LL1040-6	∅	unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:coding-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x]	Base	example		Not State	Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:exact-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:exact-start-end.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​value[x]	Base	extensible	LOINC Answer Codes for LL5323-2	∅	unknown?
Observation.component:coordinate-system.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:ref-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:ref-allele.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:ref-allele.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​value[x]	Base	required	Coding DNA Change Types Value Set	📦0.2.0	This IG
Observation.component:coding-change-type.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​value[x]	Base	extensible	LOINC Answer Codes for LL378-1	∅	unknown?
Observation.component:genomic-source-class.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator	Base	required	QuantityComparator	📍4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​value[x]	Base	extensible	LOINC Answer Codes for LL381-5	∅	unknown?
Observation.component:allelic-state.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​value[x]	Base	extensible	Variant Inheritances	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:variant-inheritance.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:variation-code.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variation-code.​value[x]	Base	example		Not State	Unknown
Observation.component:variation-code.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:variation-code.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	LOINC Answer Codes for LL2938-0	∅	unknown?
Observation.component:chromosome-identifier.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:protein-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​value[x]	Base	required	Amino Acid Change Type Value Set	📦0.2.0	This IG
Observation.component:amino-acid-change-type.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​value[x]	Base	extensible	Molecular Consequence	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:molecular-consequence.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:copy-number.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:copy-number.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:copy-number.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​value[x]	Base	required	Variant Confidence Status	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:variant-confidence-status.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​value[x]	Base	required	Clinical Relevance Value Set	📦0.2.0	This IG
Observation.component:clinical-relevance.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:nucleotides-count.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:nucleotides-count.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:nucleotides-count.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:gene-region.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-region.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:gene-region.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.

Constraints

Id	Grade	Path(s)	Description	Expression
cnt-3	error	Observation.component:copy-number.value[x]	There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.	(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both	extension.exists() != value.exists()
o-var-req-1	error	Observation	The subject element is required and must be provided.	subject.exists() and subject.resolve().is(Patient)
o-var-req-2	error	Observation	The effectiveDateTime element is required and must be provided.	effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3	error	Observation	The genes extension is required and must be provided.	component.where(code.coding.code = '48018-6').exists()
o-var-req-4	error	Observation	At least one HGVS representation (coding, protein, or genomic) must be provided.	component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text	low.exists() or high.exists() or text.exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

Summary

Mandatory: 6 elements
Must-Support: 19 elements

Structures

This structure refers to these other structures:

• Cancer Patient Profile (http://onconova.github.io/fhir/StructureDefinition/onconova-cancer-patient)

Extensions

This structure refers to these extensions:

• http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date

Key Elements View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicVariant	Variant Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
Slices for extension				Content/Rules for all slices
extension:secondary-finding		0..1	CodeableConcept	Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:genomic-variant-assessment-date	SO	0..1	dateTime	Genomic Variant Assessment Date URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
status	?!SΣ	1..1	code	Not used in this profile Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category	S	1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
coding	Σ	1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
code	SΣ	1..1	CodeableConcept	69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69548-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
subject	SOΣ	1..1	Reference(Cancer Patient Profile)	Who and/or what the observation is about Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
focus	Σ	0..*	Reference(Resource)	Not used in this profile
encounter	Σ	0..1	Reference(Encounter)	Not used in this profile
Slices for effective[x]	SΣ	1..1	dateTime	Clinically-relevant date of the genomic variant (e.g. the specimen collection date) Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SOΣ	0..1	dateTime	Clinically relevant time/time-period for observation Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
issued	Σ	0..1	instant	Not used in this profile
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Not used in this profile
Slices for value[x]	SΣC	0..1	CodeableConcept	Actual result Slice: Unordered, Closed by type:$this
value[x]:valueCodeableConcept	ΣC	0..1	CodeableConcept	Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required)
dataAbsentReason	SC	0..1	CodeableConcept	Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	Not used in this profile Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
bodySite		0..1	CodeableConcept	Not used in this profile Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method	S	0..1	CodeableConcept	Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible)
specimen	S	0..1	Reference(Human Specimen Profile)	Not used in this profile
device		0..1	Reference(Device | DeviceMetric)	Not used in this profile
Slices for component	SΣ	4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
component:conclusion-string	Σ	0..1	BackboneElement	Not used in this profile
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:gene-studied	SΣ	0..*	BackboneElement	Gene Studied
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
component:cytogenetic-location	SOΣ	0..*	BackboneElement	Cytogenetic (Chromosome) Location Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Example: 1q21.1
component:reference-sequence-assembly	OΣ	0..*	BackboneElement	Human Reference Sequence Assembly Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
component:coding-hgvs	OΣ	0..1	BackboneElement	Coding (cDNA) Change - cHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48004-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
component:genomic-hgvs	SOΣ	0..1	BackboneElement	Genomic (gDNA) Change - gHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81290-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
component:cytogenomic-nomenclature	SΣ	0..1	BackboneElement	Cytogenomic Nomenclature (ISCN)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81291-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Actual component result Binding Description: (example): Binding not yet defined
component:genomic-ref-seq	OΣ	0..1	BackboneElement	Genomic Reference Sequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48013-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned genomic reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
component:transcript-ref-seq	OΣ	0..1	BackboneElement	Reference Transcript Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 51958-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned transcript reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
component:exact-start-end	OΣ	0..1	BackboneElement	Exact Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81254-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:inner-start-end	OΣ	0..1	BackboneElement	Inner Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81302-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:outer-start-end	OΣ	0..1	BackboneElement	Outer Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81301-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:coordinate-system	OΣ	0..1	BackboneElement	Coordinate System Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 92822-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible)
component:ref-allele	Σ	0..1	BackboneElement	Not used in this profile
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69547-8
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:alt-allele	Σ	0..1	BackboneElement	Not used in this profile
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69551-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:coding-change-type	SOΣ	0..1	BackboneElement	Coding DNA Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48019-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: Coding DNA Change Types Value Set (required)
component:genomic-source-class	SOΣ	0..1	BackboneElement	Genomic Source Class Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48002-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible)
component:sample-allelic-frequency	SOΣ	0..1	BackboneElement	Sample Allelic Frequency Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81258-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	Quantity	Relative frequency in the sample
comparator	?!Σ	0..1	code	< | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented.
system	ΣC	0..1	uri	System that defines coded unit form Required Pattern: http://unitsofmeasure.org
component:allelic-read-depth	OΣ	0..1	BackboneElement	Allelic Read Depth Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82121-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
component:allelic-state	SOΣ	0..1	BackboneElement	Allelic State Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 53034-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible)
component:variant-inheritance	OΣ	0..1	BackboneElement	Variant Inheritance Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-inheritance
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Maternal | Paternal | Unknown Binding: Variant Inheritances (extensible)
component:variation-code	SOΣ	0..*	BackboneElement	Variation Code Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81252-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	ClinVar ID or similar Binding Description: (example): Multiple bindings acceptable
component:chromosome-identifier	OΣ	0..*	BackboneElement	Chromosome Identifier Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48000-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
component:protein-hgvs	SOΣ	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48005-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
component:amino-acid-change-type	SOΣ	0..1	BackboneElement	Amino Acid Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48006-1 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48006-1
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent Binding: Amino Acid Change Type Value Set (required)
component:molecular-consequence	SOΣ	0..1	BackboneElement	Molecular Consequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	molecular-consequence Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: molecular-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
component:copy-number	SOΣ	0..1	BackboneElement	Genomic Structural Variant Copy Number Obligations Actor SHALL:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82155-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣC	0..1	Quantity	Actual component result Constraints: cnt-3
component:variant-confidence-status	OΣ	0..1	BackboneElement	Variant Confidence Status Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-confidence-status
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	High | Intermediate | Low Binding: Variant Confidence Status (required)
component:clinical-relevance	SOΣ	1..1	BackboneElement	Clinical relevance of the genomic variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LL4034-6
display		1..1	string	Representation defined by the system Fixed Value: ACMG_Clinical significance of genetic variation
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	Actual component result Binding: Clinical Relevance Value Set (required)
component:nucleotides-count	SOΣ	1..1	BackboneElement	Length of of the variant in nNucleotides Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C709
display		1..1	string	Representation defined by the system Fixed Value: Nucleotides
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	integer	Actual component result
component:gene-region	SOΣ	1..1	BackboneElement	Region (exon, intron, etc.) of the gene affected by the variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova) MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C13445
display		1..1	string	Representation defined by the system Fixed Value: Gene Feature
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
component:gene-panel-sequencing	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C165600
display		1..1	string	Representation defined by the system Fixed Value: Tumor Panel Sequencing
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Sequencing Gene Panel
component:hgvs-version	SOΣ	1..1	BackboneElement	HGVS Version Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81303-0
display		1..1	string	Representation defined by the system Fixed Value: HGVS version [ID]
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
component:rna-hgvs	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: rna-hgvs
display		1..1	string	Representation defined by the system Fixed Value: Transcript RNA change (rHGVS)
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.status	Base	required	ObservationStatus	📍4.0.1	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.value[x]:valueCodeableConcept	Base	required	LOINC Answer Codes for LL1971-2	∅	unknown?
Observation.dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📦4.0.1	FHIR Std.
Observation.method	Base	extensible	LOINC Answer Codes for LL4048-6	∅	unknown?
Observation.component.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	LOINC Answer Codes for LL1040-6	∅	unknown?
Observation.component:coding-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:cytogenomic-nomenclature.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x]	Base	example		Not State	Unknown
Observation.component:genomic-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:transcript-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:exact-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​value[x]	Base	extensible	LOINC Answer Codes for LL5323-2	∅	unknown?
Observation.component:ref-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​value[x]	Base	required	Coding DNA Change Types Value Set	📦0.2.0	This IG
Observation.component:genomic-source-class.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​value[x]	Base	extensible	LOINC Answer Codes for LL378-1	∅	unknown?
Observation.component:sample-allelic-frequency.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator	Base	required	QuantityComparator	📍4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​value[x]	Base	extensible	LOINC Answer Codes for LL381-5	∅	unknown?
Observation.component:variant-inheritance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​value[x]	Base	extensible	Variant Inheritances	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:variation-code.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variation-code.​value[x]	Base	example		Not State	Unknown
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	LOINC Answer Codes for LL2938-0	∅	unknown?
Observation.component:protein-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:amino-acid-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​value[x]	Base	required	Amino Acid Change Type Value Set	📦0.2.0	This IG
Observation.component:molecular-consequence.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​value[x]	Base	extensible	Molecular Consequence	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:copy-number.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​value[x]	Base	required	Variant Confidence Status	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:clinical-relevance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​value[x]	Base	required	Clinical Relevance Value Set	📦0.2.0	This IG
Observation.component:nucleotides-count.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-region.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.

Constraints

Id	Grade	Path(s)	Description	Expression
cnt-3	error	Observation.component:copy-number.value[x]	There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.	(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both	extension.exists() != value.exists()
o-var-req-1	error	Observation	The subject element is required and must be provided.	subject.exists() and subject.resolve().is(Patient)
o-var-req-2	error	Observation	The effectiveDateTime element is required and must be provided.	effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3	error	Observation	The genes extension is required and must be provided.	component.where(code.coding.code = '48018-6').exists()
o-var-req-4	error	Observation	At least one HGVS representation (coding, protein, or genomic) must be provided.	component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

Differential View

This structure is derived from GenomicVariant

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicVariant	Variant Constraints: o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
Slices for extension				Content/Rules for all slices
extension:genomic-variant-assessment-date	SO	0..1	dateTime	Genomic Variant Assessment Date URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
status		1..1	code	Not used in this profile
subject	O	1..1	Reference(Cancer Patient Profile)	Who and/or what the observation is about Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
focus		0..*	Reference(Resource)	Not used in this profile
encounter		0..1	Reference(Encounter)	Not used in this profile
effective[x]		1..1	dateTime	Clinically-relevant date of the genomic variant (e.g. the specimen collection date)
Slices for effective[x]				Content/Rules for all slices
effective[x]:effectiveDateTime	O	0..1	dateTime	Clinically relevant time/time-period for observation Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
issued		0..1	instant	Not used in this profile
performer		0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Not used in this profile
interpretation		0..*	CodeableConcept	Not used in this profile
bodySite		0..1	CodeableConcept	Not used in this profile
specimen		0..1	Reference(Human Specimen Profile)	Not used in this profile
device		0..1	Reference(Device | DeviceMetric)	Not used in this profile
component		4..*	BackboneElement	Component results
Slices for component				Content/Rules for all slices
component:conclusion-string		0..1	BackboneElement	Not used in this profile
component:cytogenetic-location	O	0..*	BackboneElement	Cytogenetic (Chromosome) Location Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:reference-sequence-assembly	O	0..*	BackboneElement	Human Reference Sequence Assembly Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:coding-hgvs	O	0..1	BackboneElement	Coding (cDNA) Change - cHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T
component:genomic-hgvs	O	0..1	BackboneElement	Genomic (gDNA) Change - gHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup
component:genomic-ref-seq	O	0..1	BackboneElement	Genomic Reference Sequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:transcript-ref-seq	O	0..1	BackboneElement	Reference Transcript Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:exact-start-end	O	0..1	BackboneElement	Exact Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:inner-start-end	O	0..1	BackboneElement	Inner Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:outer-start-end	O	0..1	BackboneElement	Outer Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:coordinate-system	O	0..1	BackboneElement	Coordinate System Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:ref-allele		0..1	BackboneElement	Not used in this profile
component:alt-allele		0..1	BackboneElement	Not used in this profile
component:coding-change-type	O	0..1	BackboneElement	Coding DNA Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: Coding DNA Change Types Value Set (required)
component:genomic-source-class	O	0..1	BackboneElement	Genomic Source Class Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:sample-allelic-frequency	O	0..1	BackboneElement	Sample Allelic Frequency Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:allelic-read-depth	O	0..1	BackboneElement	Allelic Read Depth Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:allelic-state	O	0..1	BackboneElement	Allelic State Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:variant-inheritance	O	0..1	BackboneElement	Variant Inheritance Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:variation-code	O	0..*	BackboneElement	Variation Code Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:chromosome-identifier	O	0..*	BackboneElement	Chromosome Identifier Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:protein-hgvs	O	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys)
component:amino-acid-change-type	O	0..1	BackboneElement	Amino Acid Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
value[x]		1..1	CodeableConcept	Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent Binding: Amino Acid Change Type Value Set (required)
component:molecular-consequence	O	0..1	BackboneElement	Molecular Consequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
component:copy-number	O	0..1	BackboneElement	Genomic Structural Variant Copy Number Obligations Actor SHALL:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:variant-confidence-status	O	0..1	BackboneElement	Variant Confidence Status Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
component:clinical-relevance	SO	1..1	BackboneElement	Clinical relevance of the genomic variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LL4034-6
display		1..1	string	Representation defined by the system Fixed Value: ACMG_Clinical significance of genetic variation
value[x]	S	0..1	CodeableConcept	Actual component result Binding: Clinical Relevance Value Set (required)
component:nucleotides-count	SO	1..1	BackboneElement	Length of of the variant in nNucleotides Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C709
display		1..1	string	Representation defined by the system Fixed Value: Nucleotides
value[x]	S	0..1	integer	Actual component result
component:gene-region	SO	1..1	BackboneElement	Region (exon, intron, etc.) of the gene affected by the variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova) MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C13445
display		1..1	string	Representation defined by the system Fixed Value: Gene Feature
value[x]	S	0..1	string	Actual component result
component:gene-panel-sequencing	SO	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C165600
display		1..1	string	Representation defined by the system Fixed Value: Tumor Panel Sequencing
value[x]	S	0..1	string	Sequencing Gene Panel
component:hgvs-version	SO	1..1	BackboneElement	HGVS Version Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81303-0
display		1..1	string	Representation defined by the system Fixed Value: HGVS version [ID]
value[x]	S	0..1	string	Actual component result
component:rna-hgvs	SO	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
code	S	1..1	CodeableConcept	Type of component observation (code / type) Required Pattern: At least the following
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
system		1..1	uri	Identity of the terminology system Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
code		1..1	code	Symbol in syntax defined by the system Fixed Value: rna-hgvs
display		1..1	string	Representation defined by the system Fixed Value: Transcript RNA change (rHGVS)
value[x]	S	0..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
Documentation for this format

Terminology Bindings (Differential)

Path	Status	Usage	ValueSet	Version	Source
Observation.component:coding-change-type.​value[x]	Base	required	Coding DNA Change Types Value Set	📦0.2.0	This IG
Observation.component:amino-acid-change-type.​value[x]	Base	required	Amino Acid Change Type Value Set	📦0.2.0	This IG
Observation.component:clinical-relevance.​value[x]	Base	required	Clinical Relevance Value Set	📦0.2.0	This IG

Constraints

Id	Grade	Path(s)	Description	Expression
o-var-req-1	error	Observation	The subject element is required and must be provided.	subject.exists() and subject.resolve().is(Patient)
o-var-req-2	error	Observation	The effectiveDateTime element is required and must be provided.	effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3	error	Observation	The genes extension is required and must be provided.	component.where(code.coding.code = '48018-6').exists()
o-var-req-4	error	Observation	At least one HGVS representation (coding, protein, or genomic) must be provided.	component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()

Snapshot View

Name	Flags	Card.	Type	Description & Constraints    Filter: Bindings Constraints Obligations
Observation	C	0..*	GenomicVariant	Variant Constraints: obs-6, obs-7, o-var-req-1, o-var-req-2, o-var-req-3, o-var-req-4
id	Σ	0..1	id	Logical id of this artifact
meta	Σ	0..1	Meta	Metadata about the resource
implicitRules	?!Σ	0..1	uri	A set of rules under which this content was created
language		0..1	code	Language of the resource content Binding: CommonLanguages (preferred): A human language. Additional Bindings Purpose AllLanguages Max Binding
text		0..1	Narrative	Text summary of the resource, for human interpretation This profile does not constrain the narrative in regard to content, language, or traceability to data elements
contained		0..*	Resource	Contained, inline Resources
Slices for extension		0..*	Extension	Extension Slice: Unordered, Open by value:url
extension:secondary-finding		0..1	CodeableConcept	Secondary findings are genetic test results that provide information about variants in a gene unrelated to the primary purpose for the testing, most often discovered when [Whole Exome Sequencing (WES)](https://en.wikipedia.org/wiki/Exome_sequencing) or [Whole Genome Sequencing (WGS)](https://en.wikipedia.org/wiki/Whole_genome_sequencing) is performed. This extension should be used to denote when a genetic finding is being shared as a secondary finding, and ideally refer to a corresponding guideline or policy statement. For more detail, please see: https://ghr.nlm.nih.gov/primer/testing/secondaryfindings URL: http://hl7.org/fhir/StructureDefinition/observation-secondaryFinding Binding: GeneticObservationSecondaryFindings (extensible): Codes to denote a guideline or policy statement when a genetic test result is being shared as a secondary finding.
extension:body-structure		0..1	Reference(BodyStructure)	Target anatomic location or structure URL: http://hl7.org/fhir/StructureDefinition/bodySite
extension:genomic-variant-assessment-date	SO	0..1	dateTime	Genomic Variant Assessment Date URL: http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
modifierExtension	?!	0..*	Extension	Extensions that cannot be ignored
identifier	Σ	0..*	Identifier	Business Identifier for observation
basedOn	Σ	0..*	Reference(CarePlan | DeviceRequest | ImmunizationRecommendation | MedicationRequest | NutritionOrder | ServiceRequest)	Fulfills plan, proposal or order
partOf	Σ	0..*	Reference(MedicationAdministration | MedicationDispense | MedicationStatement | Procedure | Immunization | ImagingStudy)	Part of referenced event
status	?!SΣ	1..1	code	Not used in this profile Binding: ObservationStatus (required): Codes providing the status of an observation.
Slices for category	S	1..*	CodeableConcept	Classification of type of observation Slice: Unordered, Open by value:coding Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories.
category:labCategory		1..1	CodeableConcept	Classification of type of observation Binding: ObservationCategoryCodes (preferred): Codes for high level observation categories. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
coding	Σ	1..1	Coding	Code defined by a terminology system Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://terminology.hl7.org/CodeSystem/observation-category
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: laboratory
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text	Σ	0..1	string	Plain text representation of the concept
code	SΣ	1..1	CodeableConcept	69548-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69548-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
subject	SOΣ	1..1	Reference(Cancer Patient Profile)	Who and/or what the observation is about Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
focus	Σ	0..*	Reference(Resource)	Not used in this profile
encounter	Σ	0..1	Reference(Encounter)	Not used in this profile
Slices for effective[x]	SΣ	1..1	dateTime	Clinically-relevant date of the genomic variant (e.g. the specimen collection date) Slice: Unordered, Closed by type:$this
effective[x]:effectiveDateTime	SOΣ	0..1	dateTime	Clinically relevant time/time-period for observation Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
issued	Σ	0..1	instant	Not used in this profile
performer	Σ	0..*	Reference(Practitioner | PractitionerRole | Organization | CareTeam | Patient | RelatedPerson)	Not used in this profile
Slices for value[x]	SΣC	0..1	CodeableConcept	Actual result Slice: Unordered, Closed by type:$this
value[x]:valueCodeableConcept	ΣC	0..1	CodeableConcept	Indeterminate | No call | Present | Absent. Binding: LOINC Answer List LL1971-2 (required)
dataAbsentReason	SC	0..1	CodeableConcept	Why the result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	Not used in this profile Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
note		0..*	CodedAnnotation	Comments about the Observation that also contain a coded type
bodySite		0..1	CodeableConcept	Not used in this profile Binding: SNOMEDCTBodyStructures (example): Codes describing anatomical locations. May include laterality.
method	S	0..1	CodeableConcept	Sequencing | SNP array | PCR | Computational analysis | ... Binding: LOINC Answer List LL4048-6 (extensible)
specimen	S	0..1	Reference(Human Specimen Profile)	Not used in this profile
device		0..1	Reference(Device | DeviceMetric)	Not used in this profile
referenceRange	C	0..*	BackboneElement	Not used in this profile Constraints: obs-3
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
low	C	0..1	SimpleQuantity	Low Range, if relevant
high	C	0..1	SimpleQuantity	High Range, if relevant
type		0..1	CodeableConcept	Reference range qualifier Binding: ObservationReferenceRangeMeaningCodes (preferred): Code for the meaning of a reference range.
appliesTo		0..*	CodeableConcept	Reference range population Binding: ObservationReferenceRangeAppliesToCodes (example): Codes identifying the population the reference range applies to.
age		0..1	Range	Applicable age range, if relevant
text		0..1	string	Text based reference range in an observation
hasMember	Σ	0..*	Reference(Observation | QuestionnaireResponse | MolecularSequence)	Not used in this profile
derivedFrom	Σ	0..*	Reference(DocumentReference | ImagingStudy | Media | QuestionnaireResponse | Observation | MolecularSequence)	Related measurements the observation is made from
Slices for component	SΣ	4..*	BackboneElement	Component results Slice: Unordered, Open by pattern:code
component:All Slices				Content/Rules for all slices
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations.
value[x]	Σ	0..1		Actual component result
valueQuantity			Quantity
valueCodeableConcept			CodeableConcept
valueString			string
valueBoolean			boolean
valueInteger			integer
valueRange			Range
valueRatio			Ratio
valueSampledData			SampledData
valueTime			time
valueDateTime			dateTime
valuePeriod			Period
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:conclusion-string	Σ	0..1	BackboneElement	Not used in this profile
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	conclusion-string Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: conclusion-string
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Summary conclusion (interpretation/impression)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-studied	SΣ	0..*	BackboneElement	Gene Studied
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48018-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48018-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	The HGNC gene symbol is to be used as display text and the HGNC gene ID used as the code. If no HGNC code issued for this gene yet, NCBI gene IDs SHALL be used. Binding: HUGO Gene Nomenclature Committee Gene Names (HGNC) (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:cytogenetic-location	SOΣ	0..*	BackboneElement	Cytogenetic (Chromosome) Location Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48001-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48001-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Example: 1q21.1
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:reference-sequence-assembly	OΣ	0..*	BackboneElement	Human Reference Sequence Assembly Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	62374-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 62374-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	GRCh37 | GRCh38 | ... Binding: LOINC Answer List LL1040-6 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:coding-hgvs	OΣ	0..1	BackboneElement	Coding (cDNA) Change - cHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48004-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48004-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'c.' string, e.g. NM_005228.5:c.2369C>T Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:genomic-hgvs	SOΣ	0..1	BackboneElement	Genomic (gDNA) Change - gHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81290-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81290-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'g.' string, e.g. NC_000016.9:g.2124200_2138612dup Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:cytogenomic-nomenclature	SΣ	0..1	BackboneElement	Cytogenomic Nomenclature (ISCN)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81291-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81291-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Actual component result Binding Description: (example): Binding not yet defined
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:genomic-ref-seq	OΣ	0..1	BackboneElement	Genomic Reference Sequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48013-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48013-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned genomic reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:transcript-ref-seq	OΣ	0..1	BackboneElement	Reference Transcript Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	51958-7 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 51958-7
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Versioned transcript reference sequence identifier Binding Description: (example): Multiple bindings acceptable (NCBI or LRG)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:exact-start-end	OΣ	0..1	BackboneElement	Exact Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81254-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81254-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Range	Range in question. 'High' can be omitted for single nucleotide variants.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:inner-start-end	OΣ	0..1	BackboneElement	Inner Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81302-2 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81302-2
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Range	Imprecise variant inner-bounding range
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:outer-start-end	OΣ	0..1	BackboneElement	Outer Start-End Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	81301-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81301-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Range	Imprecise variant outer-bounding range
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:coordinate-system	OΣ	0..1	BackboneElement	Coordinate System Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	92822-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 92822-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	0-based interval counting | 0-based character counting | 1-based character counting Binding: LOINC Answer List LL5323-2 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:ref-allele	Σ	0..1	BackboneElement	Not used in this profile
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69547-8 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69547-8
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Normalized string per the VCF format.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:alt-allele	Σ	0..1	BackboneElement	Not used in this profile
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	69551-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 69551-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	string	Normalized string per the VCF format.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:coding-change-type	SOΣ	0..1	BackboneElement	Coding DNA Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48019-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48019-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	deletion | insertion | delins | SNV | copy_number_gain | copy_number_loss | ... (many) Binding: Coding DNA Change Types Value Set (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:genomic-source-class	SOΣ	0..1	BackboneElement	Genomic Source Class Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48002-0 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48002-0
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Germline | Somatic | Fetal | Likely germline | Likely somatic | Likely fetal | Unknown genomic origin | De novo Binding: LOINC Answer List LL378-1 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:sample-allelic-frequency	SOΣ	0..1	BackboneElement	Sample Allelic Frequency Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81258-6 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81258-6
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	Quantity	Relative frequency in the sample
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations Slice: Unordered, Open by value:url
value	Σ	0..1	decimal	Numerical value (with implicit precision)
comparator	?!Σ	0..1	code	< | <= | >= | > - how to understand the value Binding: QuantityComparator (required): How the Quantity should be understood and represented.
unit	Σ	0..1	string	Unit representation
system	ΣC	0..1	uri	System that defines coded unit form Required Pattern: http://unitsofmeasure.org
code	Σ	0..1	code	Coded form of the unit
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:allelic-read-depth	OΣ	0..1	BackboneElement	Allelic Read Depth Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	82121-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82121-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	0..1	Quantity	Unfiltered count of supporting reads
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:allelic-state	SOΣ	0..1	BackboneElement	Allelic State Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	53034-5 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 53034-5
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Heteroplasmic | Homoplasmic | Homozygous | Heterozygous | Hemizygous Binding: LOINC Answer List LL381-5 (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:variant-inheritance	OΣ	0..1	BackboneElement	Variant Inheritance Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-inheritance Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-inheritance
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Maternal | Paternal | Unknown Binding: Variant Inheritances (extensible)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:variation-code	SOΣ	0..*	BackboneElement	Variation Code Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	81252-9 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81252-9
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	ClinVar ID or similar Binding Description: (example): Multiple bindings acceptable
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:chromosome-identifier	OΣ	0..*	BackboneElement	Chromosome Identifier Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	48000-4 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48000-4
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	Chromosome 1 | Chromosome 2 | ... | Chromosome 22 | Chromosome X | Chromosome Y Binding: LOINC Answer List LL2938-0 (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:protein-hgvs	SOΣ	0..1	BackboneElement	Protein (Amino Acid) Change - pHGVS Obligations Actor SHALL:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48005-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48005-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'p.' string, e.g. NP_000050.2:p.(Asn1836Lys) Binding: Human Genome Variation Society (HGVS) Nomenclature (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:amino-acid-change-type	SOΣ	0..1	BackboneElement	Amino Acid Change Type Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	48006-1 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 48006-1
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	Wild type | Deletion | Duplication | Frameshift | Initiating Methionine | Insertion | Insertion and Deletion | Missense | Nonsense | Silent Binding: Amino Acid Change Type Value Set (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:molecular-consequence	SOΣ	0..1	BackboneElement	Molecular Consequence Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	molecular-consequence Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: molecular-consequence
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	1..1	CodeableConcept	stop_lost | stop_gained | inframe_insertion | frameshift_variant | ... (many) Binding: Molecular Consequence (extensible): Concepts in sequence ontology under SO:0001537.
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:copy-number	SOΣ	0..1	BackboneElement	Genomic Structural Variant Copy Number Obligations Actor SHALL:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	82155-3 Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 82155-3
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣC	0..1	Quantity	Actual component result Constraints: cnt-3
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:variant-confidence-status	OΣ	0..1	BackboneElement	Variant Confidence Status Obligations Actor SHOULD:populate-if-known Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	Σ	1..1	CodeableConcept	variant-confidence-status Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/tbd-codes-cs
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: variant-confidence-status
display		0..1	string	Representation defined by the system
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	Σ	1..1	CodeableConcept	High | Intermediate | Low Binding: Variant Confidence Status (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:clinical-relevance	SOΣ	1..1	BackboneElement	Clinical relevance of the genomic variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: LL4034-6
display		1..1	string	Representation defined by the system Fixed Value: ACMG_Clinical significance of genetic variation
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	Actual component result Binding: Clinical Relevance Value Set (required)
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:nucleotides-count	SOΣ	1..1	BackboneElement	Length of of the variant in nNucleotides Obligations Actor MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C709
display		1..1	string	Representation defined by the system Fixed Value: Nucleotides
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	integer	Actual component result
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-region	SOΣ	1..1	BackboneElement	Region (exon, intron, etc.) of the gene affected by the variant Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova) MAY:ignore Creator (Onconova) MAY:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C13445
display		1..1	string	Representation defined by the system Fixed Value: Gene Feature
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:gene-panel-sequencing	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: C165600
display		1..1	string	Representation defined by the system Fixed Value: Tumor Panel Sequencing
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Sequencing Gene Panel
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:hgvs-version	SOΣ	1..1	BackboneElement	HGVS Version Obligations Actor SHALL:populate Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://loinc.org
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: 81303-0
display		1..1	string	Representation defined by the system Fixed Value: HGVS version [ID]
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	string	Actual component result
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
component:rna-hgvs	SOΣ	0..1	BackboneElement	Component results Obligations Actor SHOULD:populate-if-known Creator (Onconova) SHOULD:persist Consumer (Onconova)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
modifierExtension	?!Σ	0..*	Extension	Extensions that cannot be ignored even if unrecognized
code	SΣ	1..1	CodeableConcept	Type of component observation (code / type) Binding: LOINCCodes (example): Codes identifying names of simple observations. Required Pattern: At least the following
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
coding		1..*	Coding	Code defined by a terminology system Fixed Value: (Complex)
id		0..1	string	Unique id for inter-element referencing
extension		0..*	Extension	Additional content defined by implementations
system		1..1	uri	Identity of the terminology system Fixed Value: http://onconova.github.io/fhir/CodeSystem/onconova-cs-tbd
version		0..1	string	Version of the system - if relevant
code		1..1	code	Symbol in syntax defined by the system Fixed Value: rna-hgvs
display		1..1	string	Representation defined by the system Fixed Value: Transcript RNA change (rHGVS)
userSelected		0..1	boolean	If this coding was chosen directly by the user
text		0..1	string	Plain text representation of the concept
value[x]	SΣ	0..1	CodeableConcept	A valid HGVS-formatted (version >= {hgvs-version component}) 'r.' string, e.g. NM_005228.5:r.2369c>t
dataAbsentReason	C	0..1	CodeableConcept	Why the component result is missing Binding: DataAbsentReason (extensible): Codes specifying why the result (Observation.value[x]) is missing.
interpretation		0..*	CodeableConcept	High, low, normal, etc. Binding: ObservationInterpretationCodes (extensible): Codes identifying interpretations of observations.
referenceRange		0..*	See referenceRange (Observation)	Provides guide for interpretation of component result
Documentation for this format

Terminology Bindings

Path	Status	Usage	ValueSet	Version	Source
Observation.language	Base	preferred	Common Languages	📦4.0.1	FHIR Std.
Observation.status	Base	required	ObservationStatus	📍4.0.1	FHIR Std.
Observation.category	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.category:labCategory	Base	preferred	Observation Category Codes	📦4.0.1	FHIR Std.
Observation.code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.value[x]:valueCodeableConcept	Base	required	LOINC Answer Codes for LL1971-2	∅	unknown?
Observation.dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.bodySite	Base	example	SNOMED CT Body Structures	📦4.0.1	FHIR Std.
Observation.method	Base	extensible	LOINC Answer Codes for LL4048-6	∅	unknown?
Observation.referenceRange.​type	Base	preferred	Observation Reference Range Meaning Codes	📦4.0.1	FHIR Std.
Observation.referenceRange.​appliesTo	Base	example	Observation Reference Range Applies To Codes	📦4.0.1	FHIR Std.
Observation.component.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:conclusion-string.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​value[x]	Base	extensible	HUGO Gene Nomenclature Committee Gene Names (HGNC)	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:gene-studied.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:gene-studied.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenetic-location.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenetic-location.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:cytogenetic-location.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​value[x]	Base	extensible	LOINC Answer Codes for LL1040-6	∅	unknown?
Observation.component:reference-sequence-assembly.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:reference-sequence-assembly.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:coding-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:coding-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:genomic-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:genomic-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​value[x]	Base	example		Not State	Unknown
Observation.component:cytogenomic-nomenclature.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:cytogenomic-nomenclature.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:genomic-ref-seq.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:genomic-ref-seq.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​value[x]	Base	example		Not State	Unknown
Observation.component:transcript-ref-seq.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:transcript-ref-seq.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:exact-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:exact-start-end.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:exact-start-end.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:inner-start-end.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:outer-start-end.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​value[x]	Base	extensible	LOINC Answer Codes for LL5323-2	∅	unknown?
Observation.component:coordinate-system.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:coordinate-system.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:ref-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:ref-allele.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:ref-allele.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:alt-allele.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​value[x]	Base	required	Coding DNA Change Types Value Set	📦0.2.0	This IG
Observation.component:coding-change-type.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:coding-change-type.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​value[x]	Base	extensible	LOINC Answer Codes for LL378-1	∅	unknown?
Observation.component:genomic-source-class.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:genomic-source-class.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​value[x].comparator	Base	required	QuantityComparator	📍4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:sample-allelic-frequency.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:allelic-read-depth.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​value[x]	Base	extensible	LOINC Answer Codes for LL381-5	∅	unknown?
Observation.component:allelic-state.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:allelic-state.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​value[x]	Base	extensible	Variant Inheritances	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:variant-inheritance.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:variant-inheritance.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:variation-code.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variation-code.​value[x]	Base	example		Not State	Unknown
Observation.component:variation-code.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:variation-code.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​value[x]	Base	required	LOINC Answer Codes for LL2938-0	∅	unknown?
Observation.component:chromosome-identifier.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:chromosome-identifier.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​value[x]	Base	required	Human Genome Variation Society (HGVS) Nomenclature	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:protein-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:protein-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​value[x]	Base	required	Amino Acid Change Type Value Set	📦0.2.0	This IG
Observation.component:amino-acid-change-type.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:amino-acid-change-type.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​value[x]	Base	extensible	Molecular Consequence	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:molecular-consequence.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:molecular-consequence.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:copy-number.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:copy-number.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:copy-number.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​value[x]	Base	required	Variant Confidence Status	📦2.0.0	Genomics Reporting Implementation Guide v2.0
Observation.component:variant-confidence-status.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:variant-confidence-status.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​value[x]	Base	required	Clinical Relevance Value Set	📦0.2.0	This IG
Observation.component:clinical-relevance.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:clinical-relevance.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:nucleotides-count.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:nucleotides-count.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:nucleotides-count.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:gene-region.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-region.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:gene-region.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:gene-panel-sequencing.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:hgvs-version.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​code	Base	example	LOINC Codes	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​dataAbsentReason	Base	extensible	DataAbsentReason	📦4.0.1	FHIR Std.
Observation.component:rna-hgvs.​interpretation	Base	extensible	Observation Interpretation Codes	📦4.0.1	FHIR Std.

Constraints

Id	Grade	Path(s)	Description	Expression
cnt-3	error	Observation.component:copy-number.value[x]	There SHALL be a code with a value of '1' if there is a value. If system is present, it SHALL be UCUM. If present, the value SHALL be a whole number.	(code.exists() or value.empty()) and (system.empty() or system = %ucum) and (code.empty() or code = '1') and (value.empty() or value.hasValue().not() or value.toString().contains('.').not())
dom-2	error	Observation	If the resource is contained in another resource, it SHALL NOT contain nested Resources	contained.contained.empty()
dom-3	error	Observation	If the resource is contained in another resource, it SHALL be referred to from elsewhere in the resource or SHALL refer to the containing resource	contained.where((('#'+id in (%resource.descendants().reference | %resource.descendants().as(canonical) | %resource.descendants().as(uri) | %resource.descendants().as(url))) or descendants().where(reference = '#').exists() or descendants().where(as(canonical) = '#').exists() or descendants().where(as(canonical) = '#').exists()).not()).trace('unmatched', id).empty()
dom-4	error	Observation	If a resource is contained in another resource, it SHALL NOT have a meta.versionId or a meta.lastUpdated	contained.meta.versionId.empty() and contained.meta.lastUpdated.empty()
dom-5	error	Observation	If a resource is contained in another resource, it SHALL NOT have a security label	contained.meta.security.empty()
dom-6	best practice	Observation	A resource should have narrative for robust management	text.`div`.exists()
ele-1	error	**ALL** elements	All FHIR elements must have a @value or children	hasValue() or (children().count() > id.count())
ext-1	error	**ALL** extensions	Must have either extensions or value[x], not both	extension.exists() != value.exists()
o-var-req-1	error	Observation	The subject element is required and must be provided.	subject.exists() and subject.resolve().is(Patient)
o-var-req-2	error	Observation	The effectiveDateTime element is required and must be provided.	effectiveDateTime.exists() and effectiveDateTime.hasValue()
o-var-req-3	error	Observation	The genes extension is required and must be provided.	component.where(code.coding.code = '48018-6').exists()
o-var-req-4	error	Observation	At least one HGVS representation (coding, protein, or genomic) must be provided.	component.where(code.coding.code = '48004-6').exists() or component.where(code.coding.code = '81290-9').exists() or component.where(code.coding.code = '48005-3').exists()
obs-3	error	Observation.referenceRange	Must have at least a low or a high or text	low.exists() or high.exists() or text.exists()
obs-6	error	Observation	dataAbsentReason SHALL only be present if Observation.value[x] is not present	dataAbsentReason.empty() or value.empty()
obs-7	error	Observation	If Observation.code is the same as an Observation.component.code then the value element associated with the code SHALL NOT be present	value.empty() or component.code.where(coding.intersect(%resource.code.coding).exists()).empty()

This structure is derived from GenomicVariant

Summary

Mandatory: 6 elements
Must-Support: 19 elements

Structures

This structure refers to these other structures:

• Cancer Patient Profile (http://onconova.github.io/fhir/StructureDefinition/onconova-cancer-patient)

Extensions

This structure refers to these extensions:

• http://onconova.github.io/fhir/StructureDefinition/onconova-ext-genomic-variant-assessment-date